<!DOCTYPE html>
<html lang="" xml:lang="">
<head>

  <meta charset="utf-8" />
  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
  <title>9 GSEA enrichment analysis | IMP: Bridging the Gap for Medicinal Plant Genomics</title>
  <meta name="description" content="9 GSEA enrichment analysis | IMP: Bridging the Gap for Medicinal Plant Genomics" />
  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />

  <meta property="og:title" content="9 GSEA enrichment analysis | IMP: Bridging the Gap for Medicinal Plant Genomics" />
  <meta property="og:type" content="book" />
  
  
  

  <meta name="twitter:card" content="summary" />
  <meta name="twitter:title" content="9 GSEA enrichment analysis | IMP: Bridging the Gap for Medicinal Plant Genomics" />
  
  
  

<meta name="author" content="Chen Tong" />
<meta name="author" content="Address: https://www.bic.ac.cn/IMP" />
<meta name="author" content="chent@nrc.ac.cn / chentong_biology@163.com" />


<meta name="date" content="2024-01-10" />

  <meta name="viewport" content="width=device-width, initial-scale=1" />
  <meta name="apple-mobile-web-app-capable" content="yes" />
  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
  
  
<link rel="prev" href="GOKEGGenrichmentanalysis.html"/>
<link rel="next" href="genemapviewer.html"/>
<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />








<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>



<style type="text/css">
  
  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
</style>

<link rel="stylesheet" href="style.css" type="text/css" />
</head>

<body>



  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">

    <div class="book-summary">
      <nav role="navigation">

<ul class="summary">
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Overview of IMP</a></li>
<li class="chapter" data-level="1" data-path="impchinese.html"><a href="impchinese.html"><i class="fa fa-check"></i><b>1</b> IMP中文版教程</a>
<ul>
<li class="chapter" data-level="1.1" data-path="impchinese.html"><a href="impchinese.html#impindex20"><i class="fa fa-check"></i><b>1.1</b> 首页信息</a></li>
<li class="chapter" data-level="1.2" data-path="impchinese.html"><a href="impchinese.html#impglobalsearch"><i class="fa fa-check"></i><b>1.2</b> 基于功能描述、注释或基因名字的全局搜索</a></li>
<li class="chapter" data-level="1.3" data-path="impchinese.html"><a href="impchinese.html#impsinglegene"><i class="fa fa-check"></i><b>1.3</b> 以单基因为中心的详情页面展示</a></li>
<li class="chapter" data-level="1.4" data-path="impchinese.html"><a href="impchinese.html#impgep"><i class="fa fa-check"></i><b>1.4</b> 多基因表达图谱</a></li>
<li class="chapter" data-level="1.5" data-path="impchinese.html"><a href="impchinese.html#genefishing135"><i class="fa fa-check"></i><b>1.5</b> Gene fishing 调取表达模式相近的基因</a></li>
<li class="chapter" data-level="1.6" data-path="impchinese.html"><a href="impchinese.html#gokegg"><i class="fa fa-check"></i><b>1.6</b> GO/KEGG 富集分析</a></li>
<li class="chapter" data-level="1.7" data-path="impchinese.html"><a href="impchinese.html#gsea-富集分析"><i class="fa fa-check"></i><b>1.7</b> GSEA 富集分析</a></li>
<li class="chapter" data-level="1.8" data-path="impchinese.html"><a href="impchinese.html#blastch"><i class="fa fa-check"></i><b>1.8</b> BLAST序列比对和搜索</a>
<ul>
<li class="chapter" data-level="1.8.1" data-path="impchinese.html"><a href="impchinese.html#blastnparameter"><i class="fa fa-check"></i><b>1.8.1</b> BLAST 参数参考</a></li>
</ul></li>
<li class="chapter" data-level="1.9" data-path="impchinese.html"><a href="impchinese.html#primerdesignch"><i class="fa fa-check"></i><b>1.9</b> 引物设计</a></li>
<li class="chapter" data-level="1.10" data-path="impchinese.html"><a href="impchinese.html#msach"><i class="fa fa-check"></i><b>1.10</b> 多序列比对展示</a></li>
<li class="chapter" data-level="1.11" data-path="impchinese.html"><a href="impchinese.html#sequencefetchch"><i class="fa fa-check"></i><b>1.11</b> 序列提取</a></li>
<li class="chapter" data-level="1.12" data-path="impchinese.html"><a href="impchinese.html#genemapviewerch"><i class="fa fa-check"></i><b>1.12</b> 基因簇可视化</a></li>
<li class="chapter" data-level="1.13" data-path="impchinese.html"><a href="impchinese.html#degeneanalysisch"><i class="fa fa-check"></i><b>1.13</b> 在线实验设计和差异基因分析</a>
<ul>
<li class="chapter" data-level="1.13.1" data-path="impchinese.html"><a href="impchinese.html#第一步实验设计确定要比较的物种和分组信息不同组织部位差异或不同处理的差异"><i class="fa fa-check"></i><b>1.13.1</b> 第一步：实验设计确定要比较的物种和分组信息（不同组织部位差异或不同处理的差异）</a></li>
<li class="chapter" data-level="1.13.2" data-path="impchinese.html"><a href="impchinese.html#第二步样品相关性评估和过滤异常样品"><i class="fa fa-check"></i><b>1.13.2</b> 第二步：样品相关性评估和过滤异常样品</a></li>
<li class="chapter" data-level="1.13.3" data-path="impchinese.html"><a href="impchinese.html#第三部设置比较组"><i class="fa fa-check"></i><b>1.13.3</b> 第三部，设置比较组</a></li>
<li class="chapter" data-level="1.13.4" data-path="impchinese.html"><a href="impchinese.html#第四步设置差异基因过滤阈值"><i class="fa fa-check"></i><b>1.13.4</b> 第四步：设置差异基因过滤阈值</a></li>
<li class="chapter" data-level="1.13.5" data-path="impchinese.html"><a href="impchinese.html#第五步概览样品信息和设置的参数这一步是提交前的信息确认"><i class="fa fa-check"></i><b>1.13.5</b> 第五步：概览样品信息和设置的参数，这一步是提交前的信息确认</a></li>
<li class="chapter" data-level="1.13.6" data-path="impchinese.html"><a href="impchinese.html#第六步差异基因分析结果报告"><i class="fa fa-check"></i><b>1.13.6</b> 第六步：差异基因分析结果报告</a></li>
</ul></li>
<li class="chapter" data-level="1.14" data-path="impchinese.html"><a href="impchinese.html#igvch"><i class="fa fa-check"></i><b>1.14</b> IGV 基因组浏览器</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="geneannotation.html"><a href="geneannotation.html"><i class="fa fa-check"></i><b>2</b> Systematic prediction and annotation of included genomes</a>
<ul>
<li class="chapter" data-level="2.1" data-path="geneannotation.html"><a href="geneannotation.html#genomeumltipleassembl"><i class="fa fa-check"></i><b>2.1</b> Species with multiple genome assembles</a></li>
<li class="chapter" data-level="2.2" data-path="geneannotation.html"><a href="geneannotation.html#genome_without_assembl"><i class="fa fa-check"></i><b>2.2</b> Species without published genome assembles</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="global_search.html"><a href="global_search.html"><i class="fa fa-check"></i><b>3</b> Global search genes by IDs, functions, and pathways</a>
<ul>
<li class="chapter" data-level="3.1" data-path="global_search.html"><a href="global_search.html#gene_detail_page"><i class="fa fa-check"></i><b>3.1</b> Gene detail page</a></li>
<li class="chapter" data-level="3.2" data-path="global_search.html"><a href="global_search.html#the-send-to-buttons"><i class="fa fa-check"></i><b>3.2</b> The send to buttons</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="browse_species_genes.html"><a href="browse_species_genes.html"><i class="fa fa-check"></i><b>4</b> Browse species and genes</a>
<ul>
<li class="chapter" data-level="4.1" data-path="browse_species_genes.html"><a href="browse_species_genes.html#structure-of-the-browse-page"><i class="fa fa-check"></i><b>4.1</b> Structure of the Browse page</a></li>
<li class="chapter" data-level="4.2" data-path="browse_species_genes.html"><a href="browse_species_genes.html#structure-of-the-species-detail-page"><i class="fa fa-check"></i><b>4.2</b> Structure of the species detail page</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="degeneanalysis.html"><a href="degeneanalysis.html"><i class="fa fa-check"></i><b>5</b> DE Gene analysis</a>
<ul>
<li class="chapter" data-level="5.1" data-path="degeneanalysis.html"><a href="degeneanalysis.html#overviewStructureform"><i class="fa fa-check"></i><b>5.1</b> Overview the structure of module page</a></li>
<li class="chapter" data-level="5.2" data-path="degeneanalysis.html"><a href="degeneanalysis.html#firststepoptionsrequiredpara"><i class="fa fa-check"></i><b>5.2</b> First step: choose options for each required parameter</a></li>
<li class="chapter" data-level="5.3" data-path="degeneanalysis.html"><a href="degeneanalysis.html#secondstepsamplecorre"><i class="fa fa-check"></i><b>5.3</b> Second step: check sample correlation profile and filter outlier samples</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="degeneanalysis.html"><a href="degeneanalysis.html#outliersampleasm"><i class="fa fa-check"></i><b>5.3.1</b> Automatical or manual detection of outlier samples</a></li>
<li class="chapter" data-level="5.3.2" data-path="degeneanalysis.html"><a href="degeneanalysis.html#interactiveheatmappca"><i class="fa fa-check"></i><b>5.3.2</b> Interactive heatmap showing sample correlation profiles</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="degeneanalysis.html"><a href="degeneanalysis.html#thirdstep"><i class="fa fa-check"></i><b>5.4</b> Third step: Set compare groups</a></li>
<li class="chapter" data-level="5.5" data-path="degeneanalysis.html"><a href="degeneanalysis.html#forthstep"><i class="fa fa-check"></i><b>5.5</b> Forth step: Set filtering thresholds for DE genes screening</a></li>
<li class="chapter" data-level="5.6" data-path="degeneanalysis.html"><a href="degeneanalysis.html#fifthstep"><i class="fa fa-check"></i><b>5.6</b> Fifth step: an overview of samples information and analysis parameter information</a></li>
<li class="chapter" data-level="5.7" data-path="degeneanalysis.html"><a href="degeneanalysis.html#degeneanalysisresultsreport"><i class="fa fa-check"></i><b>5.7</b> Sixth step: DE Gene analysis results report</a></li>
<li class="chapter" data-level="5.8" data-path="degeneanalysis.html"><a href="degeneanalysis.html#exportpdf"><i class="fa fa-check"></i><b>5.8</b> Export to PDF</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html"><i class="fa fa-check"></i><b>6</b> Gene expression profile</a>
<ul>
<li class="chapter" data-level="6.1" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#overviewStructureform2"><i class="fa fa-check"></i><b>6.1</b> Overview the structure of module page</a></li>
<li class="chapter" data-level="6.2" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#coferp13"><i class="fa fa-check"></i><b>6.2</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="6.3" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#gepdemo"><i class="fa fa-check"></i><b>6.3</b> The demo button</a></li>
<li class="chapter" data-level="6.4" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#precisefuzzy"><i class="fa fa-check"></i><b>6.4</b> The precise search and fuzy search mode</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="genefishing.html"><a href="genefishing.html"><i class="fa fa-check"></i><b>7</b> Gene fishing</a>
<ul>
<li class="chapter" data-level="7.1" data-path="genefishing.html"><a href="genefishing.html#genefishingcoferp5"><i class="fa fa-check"></i><b>7.1</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="7.2" data-path="genefishing.html"><a href="genefishing.html#networktoolkit"><i class="fa fa-check"></i><b>7.2</b> Network toolkit</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="GOKEGGenrichmentanalysis.html"><a href="GOKEGGenrichmentanalysis.html"><i class="fa fa-check"></i><b>8</b> GO/KEGG enrichment analysis</a>
<ul>
<li class="chapter" data-level="8.1" data-path="GOKEGGenrichmentanalysis.html"><a href="GOKEGGenrichmentanalysis.html#pgkea5"><i class="fa fa-check"></i><b>8.1</b> Principles of over-representation enrichment analysis</a></li>
<li class="chapter" data-level="8.2" data-path="GOKEGGenrichmentanalysis.html"><a href="GOKEGGenrichmentanalysis.html#coferp32"><i class="fa fa-check"></i><b>8.2</b> Choose options for each required parameters step by step</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html"><i class="fa fa-check"></i><b>9</b> GSEA enrichment analysis</a>
<ul>
<li class="chapter" data-level="9.1" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html#pgsea5"><i class="fa fa-check"></i><b>9.1</b> Principles of gene set enrichment analysis (GSEA)</a></li>
<li class="chapter" data-level="9.2" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html#coferp22"><i class="fa fa-check"></i><b>9.2</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="9.3" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html#gsearef"><i class="fa fa-check"></i><b>9.3</b> References</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="genemapviewer.html"><a href="genemapviewer.html"><i class="fa fa-check"></i><b>10</b> Gene map viewer</a>
<ul>
<li class="chapter" data-level="10.1" data-path="genemapviewer.html"><a href="genemapviewer.html#coferp5"><i class="fa fa-check"></i><b>10.1</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="10.2" data-path="genemapviewer.html"><a href="genemapviewer.html#oam31"><i class="fa fa-check"></i><b>10.2</b> Overlay and annotation mode</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="blast.html"><a href="blast.html"><i class="fa fa-check"></i><b>11</b> BLAST - Basic Local Alignment Search Tool</a>
<ul>
<li class="chapter" data-level="11.1" data-path="blast.html"><a href="blast.html#cusmBLAST5"><i class="fa fa-check"></i><b>11.1</b> Customizable BLAST</a></li>
<li class="chapter" data-level="11.2" data-path="blast.html"><a href="blast.html#blasthtmlresult"><i class="fa fa-check"></i><b>11.2</b> BLAST HTML results</a></li>
<li class="chapter" data-level="11.3" data-path="blast.html"><a href="blast.html#blasttableresult"><i class="fa fa-check"></i><b>11.3</b> BLAST Table results</a></li>
<li class="chapter" data-level="11.4" data-path="blast.html"><a href="blast.html#refblast"><i class="fa fa-check"></i><b>11.4</b> Reference</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="msa.html"><a href="msa.html"><i class="fa fa-check"></i><b>12</b> Multiple sequence alignment</a>
<ul>
<li class="chapter" data-level="12.1" data-path="msa.html"><a href="msa.html#sbmsa05"><i class="fa fa-check"></i><b>12.1</b> Sequences based multiple sequence alignment</a></li>
<li class="chapter" data-level="12.2" data-path="msa.html"><a href="msa.html#gtidbmsa27"><i class="fa fa-check"></i><b>12.2</b> Gene/Transcript IDs based multiple sequence alignment</a></li>
<li class="chapter" data-level="12.3" data-path="msa.html"><a href="msa.html#refmafft"><i class="fa fa-check"></i><b>12.3</b> Reference</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="sequencefetch.html"><a href="sequencefetch.html"><i class="fa fa-check"></i><b>13</b> Sequences fetch</a></li>
<li class="chapter" data-level="14" data-path="primerdesign.html"><a href="primerdesign.html"><i class="fa fa-check"></i><b>14</b> Primer design</a>
<ul>
<li class="chapter" data-level="14.1" data-path="primerdesign.html"><a href="primerdesign.html#primerdesigngeneids"><i class="fa fa-check"></i><b>14.1</b> Primer design for genes with IDs as input</a></li>
</ul></li>
<li class="chapter" data-level="15" data-path="igvbrowser.html"><a href="igvbrowser.html"><i class="fa fa-check"></i><b>15</b> IGV browser</a>
<ul>
<li class="chapter" data-level="15.1" data-path="igvbrowser.html"><a href="igvbrowser.html#vepigv"><i class="fa fa-check"></i><b>15.1</b> Visualizing expression profiles</a></li>
</ul></li>
<li class="chapter" data-level="16" data-path="download.html"><a href="download.html"><i class="fa fa-check"></i><b>16</b> Download</a></li>
<li class="divider"></li>
<li><a href="mailto:chentong_biology@163.com" target="blank">chentong_biology@163.com</a></li>

</ul>

      </nav>
    </div>

    <div class="book-body">
      <div class="body-inner">
        <div class="book-header" role="navigation">
          <h1>
            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">IMP: Bridging the Gap for Medicinal Plant Genomics</a>
          </h1>
        </div>

        <div class="page-wrapper" tabindex="-1" role="main">
          <div class="page-inner">

            <section class="normal" id="section-">
<div id="GSEAenrichmentanalysis" class="section level1 hasAnchor" number="9">
<h1><span class="header-section-number">9</span> GSEA enrichment analysis<a href="GSEAenrichmentanalysis.html#GSEAenrichmentanalysis" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Performing GSEA analysis based on <a href="https://bioconductor.org/packages/release/bioc/html/fgsea.html">fgsea</a> package.</p>
<div id="pgsea5" class="section level2 hasAnchor" number="9.1">
<h2><span class="header-section-number">9.1</span> Principles of gene set enrichment analysis (GSEA)<a href="GSEAenrichmentanalysis.html#pgsea5" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<ol style="list-style-type: decimal">
<li>Given a sorted gene lists (<code>L</code>) (normally sorted by log2 transformed fold change values)</li>
<li>Given a pathway <code>S</code> with multiple genes <code>s</code></li>
<li>The aim of GSEA is to whether check those gene <code>s</code> are ranomly distributed in list <code>L</code> or enriched in the top and botton region of gene list <code>L</code></li>
</ol>
<blockquote>
<p>Note</p>
<ol style="list-style-type: decimal">
<li><p><code>Enrichment score (ES)</code>: We calculate an enrichment score (ES) that reflects the degree to which a set S is overrepresented at the extremes (top or bottom) of the entire ranked list L. The score is calculated by walking down the list L, increasing a running-sum statistic when we encounter a gene in S and decreasing it when we encounter genes not in S. The magnitude of the increment depends on the correlation of the gene with the phenotype. The enrichment score is the maximum deviation from zero encountered in the random walk; it corresponds to a weighted Kolmogorov–Smirnov-like statistic. (directly copied from ref2)</p></li>
<li><p><code>normalized enrichment score (NES)</code>: normalize the ES for each gene set to account for the size of the set</p></li>
</ol>
</blockquote>
<p><img src="image/gsea_principles.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="coferp22" class="section level2 hasAnchor" number="9.2">
<h2><span class="header-section-number">9.2</span> Choose options for each required parameters step by step<a href="GSEAenrichmentanalysis.html#coferp22" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Just select each parameter sequentially as labeled in the figure (or simply just click the <code>Demo1</code> button).</p>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-74"></span>
<img src="image/gsea_form.png" alt="A screenshot of the one type of selection for GSEA enrichment based on KEGG annotation for all genes identified in chapter 5." width="100%" />
<p class="caption">
Figure 9.1: A screenshot of the one type of selection for GSEA enrichment based on KEGG annotation for all genes identified in chapter <a href="degeneanalysis.html#degeneanalysis">5</a>.
</p>
</div>
<p>Clicking <code>Submit</code>, after several seconds, one GSEA plot and one table are generated below.</p>
<blockquote>
<p>Note</p>
<p>Mousing over the plots would see the names of leading edge genes as well as other genes in showing pathways.</p>
</blockquote>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-75"></span>
<img src="image/gsea_result_allplots_inone.png" alt="The top plot shows the GSEA enrichment profiles of two top-enriched pathways. Vertical lines representing leading-edge genes. The bottom plot shows the rank distribution of all genes (actually only top 500 and bottom 500 genes are shown to accelerate the result loading)." width="100%" />
<p class="caption">
Figure 9.2: The top plot shows the GSEA enrichment profiles of two top-enriched pathways. Vertical lines representing leading-edge genes. The bottom plot shows the rank distribution of all genes (actually only top 500 and bottom 500 genes are shown to accelerate the result loading).
</p>
</div>
<blockquote>
<p>Note</p>
<p>Users are allowed to choose which enriched terms to be visualized in the GSEA plot.</p>
<p>Also the visualization ways could be changed.</p>
</blockquote>
<p><img src="image/gsearesultinoneplot.png" width="100%" style="display: block; margin: auto;" /></p>
<blockquote>
<p>Note</p>
<p>Users could check gene detail information by clicking gene names in the enrichment table.</p>
</blockquote>
</div>
<div id="gsearef" class="section level2 hasAnchor" number="9.3">
<h2><span class="header-section-number">9.3</span> References<a href="GSEAenrichmentanalysis.html#gsearef" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<ol style="list-style-type: decimal">
<li>Fast gene set enrichment analysis. Gennady Korotkevich, Vladimir Sukhov, Nikolay Budin, Boris Shpak, Maxim N. Artyomov, Alexey Sergushichev doi: <a href="https://doi.org/10.1101/060012" class="uri">https://doi.org/10.1101/060012</a></li>
<li>Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov September 30, 2005 <a href="https://doi.org/10.1073/pnas.050658010" class="uri">https://doi.org/10.1073/pnas.050658010</a></li>
</ol>

</div>
</div>
            </section>

          </div>
        </div>
      </div>
<a href="GOKEGGenrichmentanalysis.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
<a href="genemapviewer.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
    </div>
  </div>
<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
<script>
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": false,
"twitter": false,
"linkedin": false,
"weibo": false,
"instapaper": false,
"vk": false,
"whatsapp": false,
"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
},
"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
},
"edit": {
"link": null,
"text": null
},
"history": {
"link": null,
"text": null
},
"view": {
"link": null,
"text": null
},
"download": ["IMPdoc.pdf"],
"search": {
"engine": "fuse",
"options": null
},
"toc": {
"collapse": "subsection"
}
});
});
</script>

<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
  (function () {
    var script = document.createElement("script");
    script.type = "text/javascript";
    var src = "true";
    if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML";
    if (location.protocol !== "file:")
      if (/^https?:/.test(src))
        src = src.replace(/^https?:/, '');
    script.src = src;
    document.getElementsByTagName("head")[0].appendChild(script);
  })();
</script>
</body>

</html>
